BN1959 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.5496e-04 1.0380e-02
Layer 6 7.2754e-04 2.9836e-03
Layer 2 8.9402e-04 2.1850e-02
Layer 5 1.2267e-03 2.5041e-03
Layer 4 1.2994e-03 2.9686e-03
WM 1.0266e-02 9.5786e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.8340 0.6965
SNAP25 Layer 4 2.8086 0.6463
NORAD Layer 4 2.5840 0.6013
PRNP Layer 4 3.1191 0.5887
PPIA Layer 5 2.3652 0.5887
RTN3 Layer 4 2.6191 0.5831
SLC17A7 Layer 5 2.4453 0.5820
CFL1 Layer 4 2.8145 0.5815
EIF4A2 Layer 5 2.3398 0.5810
KLC1 Layer 4 2.5117 0.5808
SYT1 Layer 4 2.9082 0.5804
TSPYL1 Layer 4 2.9082 0.5800
ARPP19 Layer 2 2.4297 0.5765
GHITM Layer 5 2.4238 0.5753
RTN1 Layer 4 2.8594 0.5705
TUBB2A Layer 4 2.7910 0.5699
OLFM1 Layer 2 2.7070 0.5690
CCK Layer 6 2.4395 0.5659
NRGN Layer 4 2.8594 0.5655
YWHAG Layer 4 3.0117 0.5652
GPM6A Layer 4 2.4023 0.5648
VAMP2 Layer 6 2.3652 0.5613
SYN2 Layer 5 2.7656 0.5609
STMN1 Layer 4 2.9160 0.5585
DNM1 Layer 5 2.5117 0.5584
SULT4A1 Layer 5 2.3965 0.5575
GJA1 Layer 4 2.4609 0.5557
STXBP1 Layer 4 3.2578 0.5557
ATP5F1B Layer 4 2.6133 0.5548
MTPN Layer 2 1.9492 0.5540
NDFIP1 Layer 5 2.6953 0.5537
RAB6B Layer 4 2.5332 0.5530
LMO4 Layer 6 2.4570 0.5530
TAGLN3 Layer 6 2.3750 0.5526
ATP5F1A Layer 4 2.6543 0.5515
CAMK2A Layer 6 2.2070 0.5510
DPYSL2 Layer 4 2.6543 0.5504
CPLX1 Layer 5 2.4844 0.5504
CALM3 Layer 4 2.4395 0.5488
STMN2 Layer 5 2.7969 0.5468
UCHL1 Layer 5 3.1387 0.5460
SYN1 Layer 5 2.4844 0.5460
ATP1B1 Layer 5 2.6660 0.5453
SERINC1 Layer 4 2.8145 0.5440
TSC22D1 Layer 5 2.7246 0.5435
SLC1A2 Layer 4 2.9414 0.5431
CALM2 Layer 5 2.2227 0.5430
YWHAZ Layer 2 2.2646 0.5428
SEZ6L2 Layer 4 2.4883 0.5417
PGRMC1 Layer 6 2.0859 0.5412

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1959
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1959_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1959/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1959/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1959/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1959/report/PD/BN1959_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1959/report/PD/BN1959_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:10:56
  • Number of Processes: 10
  • Spending Time: 0h 3m